Enzymes and Biocatalysis

Course manual 2023/2024

Course content

Within the course Enzymes and Biocatalysis, the student will acquire and apply knowledge of the principles of enzyme catalysis and mechanism and related cofactors. Insight on state-of-the-art theory and methods for recombinant enzyme production and engineering will be provided, also including the modern utilization of unnatural amino acids. The current impact and potential of enzymes to solve contemporary issues of efficient chemical synthesis and sustainability will be highlighted in specific lectures. Natural photosynthesis will also be covered as a topic of contemporary importance (i.e., learn from nature how to capture and utilize light for various purposes).

Topics are listed below in detail:

1) Introduction to enzymes and biocatalysis (enzymes classification, enzymology, mechanisms in enzyme catalysis).

2) Function of cofactors, coenzymes, prosthetic groups (e.g., metals) in enzyme catalysis (including protein-based enzymes and RNAzymes).

3) Theory and technics for recombinant enzyme production.

4) Enzyme engineering (directed evolution, and semi-rational and rational engineering).

5) Unnatural amino acids in enzymes and biocatalysis.

6) Natural photosynthesis.

7) Application of enzymes to solve contemporary sustainable issues.

8) Application of enzymes for chemical synthesis.

Study materials

Literature

• Textbook: Stryer (Biochemistry ) (chapter 2, chapter 3, chapter 8, chapter 9, chapter 19) 

Other

• specific material that will be available in Canvas

Objectives

• The student is able to classify enzyme families based on type of reaction, substrate converted, cosubstrate and cofactor involved, eventually formed coproduct.
• The student is able to explain and sketch the mechanism of selected enzymatic reactions.
• The student is able to analyze the chemical structure of a cofactor and correlate it to the biochemical function.
• The student is able to explain the different functions and roles of metal-based and organic molecule-based cofacors in enzymatic reactions.
• To define the fundamental terminology in molecular biology.
• The student is able to summarize the steps for the preparation of an enzyme in the lab.
• The student is able to illustrate principles and methods in enzyme engineering and analyse pros and cons for each method.
• The student is able to illustrate principles and methods for the generation of artificial enzymes.
• The student is able to evaluate the potential role of non-natural amino acid in the context of new-to-nature enzymatic reactions.
• To understand the fundamental principle of the photosynthesis.
• To analyze current and potential future applications of enzymes in the context of sustainability and bioremediation.
• To analyze current and potential future applications of enzymes in the context of synthetic organic chemistry.

Teaching methods

• Lecture
• Presentation/symposium
• Self-study
• Tutorial

Lectures: hoorcollege in topics 1-8 (see global description). Skills trained: see all objectives 1-12.

Presentation/symposium: a team of two students choose a particular enzyme (among given options) and search for general structure, function, protein engineering and selected application(s). Then, they prepare a presentation for the students' symposium. Skills trained: see objectives 2, 3, 4, 11 and 12.

Tutorial: these will be 4 sessions of two hours each in which problems will be presented to the students. Students will try to solve them in small groups while the lecturer will provide feedback on the solutions and, when needed, additional explanations. Skills trained: see all objectives 1-12.

Learning activities

Attendance

Programme's requirements concerning attendance (OER-B):

• Active participation is expected of each student in the course for which he is registered.
• If a student cannot attend an obligatory part of a programme's component due to circumstances beyond his control, he must report in writing to the teacher in question as soon as possible. The teacher, if necessary after consulting the study adviser, may decide to issue the student a replacing assignment.
• It is not allowed to miss obligatory parts of the programme's component if there is no case of circumstances beyond one's control.
• In case of participating qualitatively or quantitatively insufficiently, the examiner can expel a student from further participation in the programme's component or a part of that component. Conditions for sufficient participation are fixed in advance in the study guide and/or on Canvas.

Additional requirements for this course:

Recommended (desirable) prior knowledge

Recommended previous attendance and pass of following courses:

Chemistry of Life (1st year), Bioorganic Chemistry (2nd year), Biochemistry (2nd year)

Assessment

Tentamen: Written final exam (70% of the final grade). It will be based on the content of the Hoorcollege (20 hours). The students will have the opportunity to practise and prepare for the final exam during the tutorials.

Presentation symposium (30% of the final grade): a team of two students choose a particular enzyme (among given options) and search for general structure, function, protein engineering and selected application(s). Then, they prepare a presentation for the students' symposium.

Inspection of assessed work

Canvas

Assignments

Presentation symposium as mentioned above: a team of two students choose a particular enzyme (among given options) and search for general structure, function, protein engineering and selected application(s). Then, they prepare a presentation for the students' symposium.

Fraud and plagiarism

The 'Regulations governing fraud and plagiarism for UvA students' applies to this course. This will be monitored carefully. Upon suspicion of fraud or plagiarism the Examinations Board of the programme will be informed. For the 'Regulations governing fraud and plagiarism for UvA students' see: www.student.uva.nl

Course structure

Timetable

The schedule for this course is published on DataNose.

Contact information

Coordinator

• dr. Francesco Mutti